A pterodactyl FB entered cavern level 1 (F5 hotkey) which I thought I had sealed off. However, the beast still managed to get into my fort, and I can't figure out how.

The combat reports for Uja the Forgotten Beast show him attacking a goose in the caverns, then later a rabbit inside the fort. But unless I missed something, the entire stairwell down into the caverns is sealed off completely with natural and constructed walls and floors, with a few (still intact) grates for water access.